.. _practice_slicer:

Practice Slicer
---------------

In this part of the lab, you will exercise with Slicer_. Follow the steps:

- Find a convenient 3D image dataset (MRI, CT for instance). Ideally it should be a personal dataset. It will be more fun. Otherwise, there are plenty of datasets available on the net. **Do not use** the datasets that Slicer provides in the welcome page.

- Open it with Slicer_. Explore the data. Browse the images. Try to understand what you are looking at. Read the diagnosis if you have it, or any complementary information from the website where you took the dataset if you found it on the net. Put a name to the structures (e.g. If you have a bone, identify its name. Is it a tibia or a femur?). Look for a medical illustration that will help you to name the structures. Check the resolution of the model, the number of bytes per voxel, the spatial resolution of the pixels and the interslice distance. Is the volume (in mm³) consistent with the volume of the real structure of the object you are looking at? For instance, if you are looking at a head, what is the expected volume?

- Play with the transfer function. Find transfer functions that will allow you to see some or all the interesting features. Think why you are getting a particular image taking into account how you have designed the transfer function. Save the best two images and their transfer functions. 

- Segment and extract one or more polygonal surfaces of a structure of interest (bone, skin, muscle, an organ, a blood vessel, a tumor...). Experiment with different segmentation methods, not only threshold. Play with the surface rendering parameters and save one or two images. Write down the number of vertices and faces of these meshes. Write down their area.

- Create one nice picture or animation integrating the rendering of the polygonal meshe(s) and the volume. Eventually, add a 2D slice on top. This picture should help us to understand and contextualize the reason why the 3D images were initially captured.

- Prepare a 5 to 6 slides of presentation of this work. You will have 5 minutes to expose it orally in English (**very strict timing**).



Slides
~~~~~~

  * See theory slides: slides-7_, slides-8_, slides-9_


.. _slides-7: https://www.cs.upc.edu/~dani/IM/session7.pdf
.. _slides-8: https://www.cs.upc.edu/~dani/IM/session8.pdf
.. _slides-9: https://www.cs.upc.edu/~dani/IM/session9.pdf
.. _slicer: https://www.slicer.org